Create stub pages (icbi-lab#1)

data

@@ -0,0 +1 @@
+/data/projects/2023/atlas_protocol

docs/index.md

@@ -6,11 +6,16 @@
 :hidden: true
 :maxdepth: 1
 
+notebooks/01_qc.ipynb
+notebooks/02_seed_annotation.ipynb
+notebooks/03_merge.ipynb
+notebooks/04_integrate_scvi.ipynb
+notebooks/05_cell_type_annotation.ipynb
+
 api.md
 changelog.md
 template_usage.md
 contributing.md
 references.md
 
-notebooks/example
 ```

docs/notebooks/01_qc.ipynb

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+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Quality control and filtering\n",
+    "\n",
+    "```{note}\n",
+    "**datasets vs. studies**: By “study”, we refer to a scientific publication, while with “dataset”, \n",
+    "we refer to a set of samples that was generated using the same sequencing platform and processed in the same way.\n",
+    "One study may contain one or multiple datasets. Datasets must be processed independently. \n",
+    "```"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/notebooks/02_seed_annotation.ipynb

@@ -0,0 +1,20 @@
+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Seed annotation"
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/notebooks/03_merge.ipynb

@@ -0,0 +1,25 @@
+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Merge data and harmonized annotations"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/notebooks/04_integrate_scvi.ipynb

@@ -0,0 +1,27 @@
+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Integrate data and perform doublet detection"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/notebooks/05_cell_type_annotation.ipynb

@@ -0,0 +1,25 @@
+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Cell-type annotation"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}